Variant report

Variant	rs11140189
Chromosome Location	chr9:72377357-72377358
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:72375672..72377949-chr9:72385605..72387785,2	K562	blood:

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10780598	0.84[ASW][hapmap];0.96[CEU][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10867952	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10867966	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10867987	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10868033	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10868041	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11139997	1.00[ASW][hapmap];0.96[CEU][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11140181	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11140185	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140204	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140205	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140206	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140208	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11791457	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11792104	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11793130	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12376529	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13287102	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13293591	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13293770	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1411411	1.00[CHB][hapmap];0.92[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1536993	0.81[CEU][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.86[AMR][1000 genomes]
rs2026795	0.84[ASW][hapmap];0.96[CEU][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3904635	0.83[AMR][1000 genomes]
rs4273913	0.86[AMR][1000 genomes]
rs56040923	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7027072	0.83[AMR][1000 genomes]
rs7866040	0.84[AMR][1000 genomes]
rs918337	0.96[CEU][hapmap];0.93[JPT][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471309	chr9:72273898-72410323	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv1050920	chr9:72345297-72579301	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv831611	chr9:72361905-72512134	Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv893438	chr9:72363992-72720438	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11140189	PTAR1	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72375400-72377400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr9:72375400-72377800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr9:72375400-72379200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr9:72375600-72377400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr9:72375600-72377400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr9:72375600-72377400	Weak transcription	NHDF-Ad	bronchial
7	chr9:72375600-72377600	Weak transcription	Right Atrium	heart
8	chr9:72375600-72379000	Weak transcription	Fetal Intestine Large	intestine
9	chr9:72375600-72379000	Weak transcription	Fetal Kidney	kidney
10	chr9:72375600-72383000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr9:72375600-72383200	Weak transcription	HSMMtube	muscle
12	chr9:72375800-72377400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr9:72375800-72377400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr9:72375800-72377400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr9:72375800-72377400	Weak transcription	A549	lung
16	chr9:72375800-72377400	Weak transcription	NH-A	brain
17	chr9:72375800-72377400	Weak transcription	Osteobl	bone
18	chr9:72375800-72378000	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr9:72375800-72379000	Weak transcription	HepG2	liver
20	chr9:72376400-72377600	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr9:72376400-72377800	Enhancers	H1 Cell Line	embryonic stem cell
22	chr9:72376600-72377400	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr9:72376600-72377400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr9:72376800-72378800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr9:72377000-72377400	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr9:72377000-72377400	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr9:72377000-72377600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr9:72377000-72378000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr9:72377000-72378200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr9:72377200-72378000	Enhancers	Muscle Satellite Cultured Cells	--
31	chr9:72377200-72378000	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr9:72377200-72378200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
33	chr9:72377200-72378200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr9:72377200-72383400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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